diff --git a/developer-doc/PlumedDeveloperHeader.html b/developer-doc/PlumedDeveloperHeader.html
index f3384bf853a6a9b2d950bdd6e2244ba9c1921705..4a231fa501d8168197a8d0d320ba4f5cd12bd58c 100644
--- a/developer-doc/PlumedDeveloperHeader.html
+++ b/developer-doc/PlumedDeveloperHeader.html
@@ -7,21 +7,20 @@
<meta name="generator" content="Doxygen $doxygenversion"/>
<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
-<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
-<script type="text/javascript" src="$relpath^jquery.js"></script>
-<script type="text/javascript" src="$relpath^dynsections.js"></script>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
$treeview
$search
$mathjax
-<link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
-$extrastylesheet
+<link href="$stylesheet" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<!--BEGIN TITLEAREA-->
<div id="titlearea">
-<table cellspacing="0" cellpadding="0">
+<table align="center" frame="void" width="98%" cellpadding="2%">
<tbody>
<tr style="height: 30px;">
<td valign="center"> <img src="../pigeon.png" width="120"/></td>
diff --git a/developer-doc/PlumedFooter.html b/developer-doc/PlumedFooter.html
index 04224dca77845a55f597aabddece9120a3ca81e4..00e1a56ede3032b6affbcf89d8fa5839f11d1c3b 100644
--- a/developer-doc/PlumedFooter.html
+++ b/developer-doc/PlumedFooter.html
@@ -12,13 +12,13 @@
<!--END GENERATE_TREEVIEW-->
<!--BEGIN !GENERATE_TREEVIEW-->
<hr class="footer"/><address class="footer"><small>
-<table>
+<table align="center" frame="void" width="98%" cellpadding="2%">
<tr><td align="left" valign="center">
Hosted by
<a href="http://developer.berlios.de"><img src="http://developer.berlios.de/bslogo.php?group_id=11362" width="124" height="32" alt="BerliOS Logo" /></a>
<!--$generatedby   --> <a href="http://www.doxygen.org/index.html">
-</td><td width=88% align="right">
-<img class="footer" src="$relpath^doxygen.png" alt="doxygen" align="right"/>
+</td><td width=90% align="right">
+<img class="footer" src="doxygen.png" alt="doxygen" align="right"/>
</a> $doxygenversion
</td> </tr>
</table>
diff --git a/user-doc/PlumedFooter.html b/user-doc/PlumedFooter.html
index 04224dca77845a55f597aabddece9120a3ca81e4..00e1a56ede3032b6affbcf89d8fa5839f11d1c3b 100644
--- a/user-doc/PlumedFooter.html
+++ b/user-doc/PlumedFooter.html
@@ -12,13 +12,13 @@
<!--END GENERATE_TREEVIEW-->
<!--BEGIN !GENERATE_TREEVIEW-->
<hr class="footer"/><address class="footer"><small>
-<table>
+<table align="center" frame="void" width="98%" cellpadding="2%">
<tr><td align="left" valign="center">
Hosted by
<a href="http://developer.berlios.de"><img src="http://developer.berlios.de/bslogo.php?group_id=11362" width="124" height="32" alt="BerliOS Logo" /></a>
<!--$generatedby   --> <a href="http://www.doxygen.org/index.html">
-</td><td width=88% align="right">
-<img class="footer" src="$relpath^doxygen.png" alt="doxygen" align="right"/>
+</td><td width=90% align="right">
+<img class="footer" src="doxygen.png" alt="doxygen" align="right"/>
</a> $doxygenversion
</td> </tr>
</table>
diff --git a/user-doc/PlumedLayout.xml b/user-doc/PlumedLayout.xml
index 4b1f0fc0342101981c750129df182fd8d0f48254..e90c76b313ceaa11bbadb8a0859c26db62acb830 100644
--- a/user-doc/PlumedLayout.xml
+++ b/user-doc/PlumedLayout.xml
@@ -21,7 +21,6 @@
<tab type="filelist" visible="yes" title="" intro=""/>
<tab type="globals" visible="yes" title="" intro=""/>
</tab>
- <tab type="dirs" visible="yes" title="" intro=""/>
<tab type="examples" visible="yes" title="" intro=""/>
</navindex>
diff --git a/user-doc/PlumedUserHeader.html b/user-doc/PlumedUserHeader.html
index 483acb912b65bf2dffe5275bfe3cea82b2848601..d337fb1b4d798d2f70cc7e0f1d8655874331ceb3 100644
--- a/user-doc/PlumedUserHeader.html
+++ b/user-doc/PlumedUserHeader.html
@@ -7,21 +7,20 @@
<meta name="generator" content="Doxygen $doxygenversion"/>
<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
-<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
-<script type="text/javascript" src="$relpath^jquery.js"></script>
-<script type="text/javascript" src="$relpath^dynsections.js"></script>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
$treeview
$search
$mathjax
-<link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
-$extrastylesheet
+<link href="$stylesheet" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<!--BEGIN TITLEAREA-->
<div id="titlearea">
-<table cellspacing="0" cellpadding="0">
+<table align="center" frame="void" width="98%" cellpadding="2%">
<tbody>
<tr style="height: 30px;">
<td valign="center"> <img src="../pigeon.png" width="120"/></td>